An analysis was done of the patterning of genetic distances between female lineages of rhesus macaques (Macaca mulatta) on Cayo Santiago. The distances (Nei, 1972) were calculated pairwise between all lineages using data from the G, H, I, J, K, L, P and Q blood group systems. Distances between lineages were found to be greater in 1972 than in 1976. Partial correlation coefficients were computed between genetic distances and troop boundaries, controlling for the combined size of the lineages being paired. None of the variance in genetic distances was explained by whether paired lineages were in the same or in different troops. A hypothesis of lineage-specific mating is offered as one explanation of the continued genetic differentiation between lineages within each troop.